Description

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘6973’ ]

assembly:file

assembly fasta file

gxdb:file

The NCBI GenBank database to search against.

Output

name:type
description
pattern

fcs_gx_report

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘9606’ ]

out/*.fcs_gx_report.txt:file

Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)

*.fcs_gx_report.txt

taxonomy_report

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘9606’ ]

out/*.taxonomy.rpt:file

Report containing the contig identifier and mapped contaminant species

*.taxonomy.rpt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

fcs

"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."